Friday, December 18, 2009

What do you use for your DNA and protein sequence analysis ?

DNA and protein sequence analysis software are routinely used in molecular biology labs.

Sequence assembly, alignments, primer design, in silico cloning and many other tools are now included as part of most software packages for sequence analysis and data management.

I've prepared a little poll to check the software preferences of the readers of MolBio Research Highlights.

[Image credit: Biology Reference]

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Anonymous said...

Difficult to answer this poll, since I use different pieces of software for different tasks. For viewing and editing protein and DNA sequence alignments, I use Jalview. For dealing with DNA sequencing trace files & manually correcting base calls, have used Chromas or FinchTV in the past, and more recently UGENE. Designing primers for cloning, I generally use a text editor (eg, vim or gVim) ... but then I suspect I'm a luddite in that respect.

I'd like to play with VectorNTI a little more, but the licensing and lack of proper cross-platform support (eg, no Linux version, last time I checked) make it not worth the hassle.

Alejandro Montenegro-Montero said...

I agree, but I guess I only wanted to know what people mainly use for their sequence analysis.

We could generate a new poll asking for items independently, like "what do you use for sequence alignment", "what do you use for primer design", etc.
That poll could give a lot of info but I don't know that many different softwares, so input from the community on different tools that could be included in the poll, would be great.